"We are interested in understanding how genomes evolve, and how genomic variation impacts phenotypic variation, adaptation, and evolution of traits"

Lab updates

October

• Hectic month! Another salmon microbiome paper hot from the press led by Shashank Gupta. We show zero impact on the microbiome of salmon using low levels of beta-manna in the feed, but propose future functional feed directions based on the salmon microbial genome atlas. Read the paper in Communication Biology. 

• Congratulations to everyone involved in Elixir-Norway (elixir.no). We were awarded a new Norwegian national infrastructure project to keep up our good work on bioinformatics infrastructure to support life science research and its translation to medicine, environment, the bioindustries and society.

• Woop-woop! New paper in Nature Microbiology. The paper led by Arturo Vera-Ponce de León is the first large scale characterisation of the genomes of the Atlantic salmon gut microbiota. Check out the paper here, and a news story here. 

• Two new PhD opportunities linked to the lab!
  • Torgeir Hvidsten and myself are seeking a PhD-student within comparative evolutionary genomics to work on our newly funded ThreeD NRC FRIPRO project. More details about the position here.
  • We also recruiting for a MSCA doctoral network PhD-position. This is another collaborative project, this time with Garett Difford, on host-microbiome interactions related to feed efficiency in salmon. More details about the position here. 

September

• NMBU have launched a new website - 'lakseløftet' - where we have gathered all information related to our efforts to increase sustainability of the salmon aquaculture industry. Check it out here. 

• We submitted a grant proposal together with the Veterinary faculty to fund SalSafe - a centre for research driven innovation. If funded, the goal is to improve welfare and reduce mortality through innovations in the salmonid aquaculture production cycle. Thanks to Marit Stormoen, Gareth Difford, Ida Beitnes Johansen for pulling this together. 

• Our Doctoral Network on microbiome-host interactions HoloGen has kicked off! (funded by the Marie Curie Action). Follow us on social media (X: @HoloGen_MSCA, Bluesky: @hologen.bsky.social, LinkedIn: www.linkedin.com/company/hologen-network) or read more on our website https://www.hologen-network.eu. 

August

• A new preprint is out: Transcriptomic profiling of gill biopsies to define predictive markers for seawater survival in farmed Atlantic salmon. We produced 3000 gill transcriptomes and tried to predict the future growth and welfare status. Read how this endeavour went here.
  

June

• Fantastic news! We got a four year 1M EUR project funded from the Norwegian Research Council on the 3D genome evolution following whole genome duplication in Atlantic salmon. Looking forward to this adventure with lots of great colleagues: Jonas Paulsen (UiO), Torgeir Hvidsten/Chris Henkel/Matthew Kent/Lars Grønvold/Hien Thu (NMBU), and Juan Tena (CABD, Sevilla, Spain). 

• Our very talented master student Eline Furseth defended her thesis today (June 4th) on the 3D genome architecture of the Atlantic salmon genome. Fantastic job, Eline!! And thanks to Mark Ravinet (University of Oslo) for being a great thesis opponent. 

• New preprint! (well, its not that new, but I forgot to post something about it back in March). Shashank (Gupta), a former postoc at KBM in the ImprovAFish project, did a great job on putting this nice paper together: The need for high-resolution gut microbiome characterization to design efficient strategies for sustainable aquaculture production. Read the paper here.

May

• We have a new preprint out from the Synchrosmolt project. The paper is about how different light regimes during development of seawater adapted salmon (smoltification) impacts salmon physiology and growth in the sea. The study is led by Bjarne Gjerde at NOFIMA. Read the paper here.

April

• Our work on the remodelling of the liver genome regulation through Atlantic salmon smolt development has now been published in PLoS ONE. We show that photoperiodic history does not have a long term impact on the livers of developing smolt (as opposed to what happens in the gill) and identify many novel transcription factors involved in the massive gene expression remodelling during this developmental transition. Read the paper here. 

March 

• I gave a talk for the EvoGene-section at UiO on our work on TEs and evolution of cis-regulatory elements (read it here). Thanks to Rein Aasland, Paul Grini and Jonas Paulsen for inviting me!

February 

• We have a new peer-revied paper out in Aquaculture - thanks to Tom Harvey and Hanne Dvergedal for leading this study! Linking genomic prediction of fillet fat content in Atlantic salmon to underlying changes in lipid metabolism regulation. Read it here.

January 2024 (happy new year!)

• Action packed January! Happy to have contributed to a really fascinating study of maternally programmed seasonal plasticity in Siberian hamsters led by the superb Shona Woods (The Arctic University of Norway). Our contribution was on the genome side (of course). The paper is out in Current Biology. Read it here.  

• Check out this new pre-print on the Atlantic salmon gut microbial genome atlas. A great collaboration between an awesome microbiome team, great bioinformaticians, and salmon biologists. Read it here.

• We have posted a new pre-print on "The role of transposon activity in shaping cis-regulatory element evolution after whole genome duplication". This work has been led by my former PhD-student Øystein Monsen (now at University in Bergen) and Lars Grønvold. Read it here. 

November 2023

• Ida Beitnes Johansen and myself published an opinion piece in DN on production of smolts and animal welfare. Read it here (only in Norwegian) 

• We have a new lab-member. Welcome Cathrine Brekke! Cathrine will be working on the genetics of gut microbial composition. Are there salmon genes that can impact which microbes that thrive in the salmon gut? 

August 2023

• Another preprint is out on bioRxiv. This one is about genetic mechanisms underlying differences in fat content in salmon muscle. We show that lean and fat fish differ in the regulation of genes involved in lipid synthesis and breakdown in liver. Moreover, we identified genetic variation impacting expression of genes, including evidence of a few strong eQTLs (one is not so far from a key transcription factor for 'lipidy' processes). Read the paper here.

• Congratulations to Line L. Røsæg who defended her PhD-thesis in style on the molecular processes involved in developmental transitions in Atlantic salmon. We are so proud of you!

• We have a new preprint out: The genome regulatory landscape of Atlantic salmon liver through smoltification | bioRxiv. Combining transcriptomics (RNA-seq), DNA-methylation quantification (RRBS) and sequencing of accessible chromatin (ATAC-seq) we characterize the dynamic regulation of the liver-genome across the transformation from a fresh- to salt-water fish. Great work by Tom Harvey, Gareth Gillard, Line Røsæg and several other in the lab!

June 2023

• YES! We were awarded 1M EUR from the Norwegian Research Council to study a genetic variant in Atlantic salmon that impact the development of sea-water physiology (smoltification) in a photoperiod dependent manner. Project lead is David Hazlerigg at UiT and the Arctic Seasonal Timekeeping Initiative. The NMBU team consists of my research group, Ida Beitnes Johansen and Turid Mørkøre.

May 2023

• Congratulations to all the fantastic master students associated with the lab on submitting their MSc thesis today!! (15th of May). So many cool projects, ranging from smolt biology, machine learning methods to predict cis regulatory elements, fungal genomics, population genetics in ash trees, and development og CRISPR editing methods. If you are interested, you can find links to the theses here.

March 2023

• We have two more papers accepted in G3.
  • In the first study Thomas Harvey led a really nice study to optimize transfection of RNPs and plasmids in primary hepatocytes in Atlantic salmon (read it here).
  • In the second study Matilde M. Holen led a nice study of the evolution and functional diversification of chitinase metabolism genes in Atlantic salmon following a whole genome duplication. (read it here)

February 2023

• Our paper on regulatory activity of transposable elements in Altantic salmon is out in G3 (read it here).

  
  

December 2022

• We congratulate Dr. Øystein Monsen with a very sucsessfull PhD-defence on the role of repeat-DNA in genome evolution. 

October 2022

• Another new pre-print is out! The lab's first attempt to study the contribution of TEs to gene regulatory evolution after whole genome duplication. The very talented master student Hanna Sahlström made use of the optimized protocol for transfection of primary hepatocytes in Atlantic salmon (see link in the post below) performed a series of reporter assays on candidate TE-cis regulatory elements. (link to the pre-print here)

• New pre-print out. Optimized protocols for transfection of DNA-vectors and CRISPR RNPs into  Atlantic salmon liver primary cells. Thanks to Ragnhild Wilberg, Alex Datsomor, and Tom Harvey for leading this work. 

August 2022

• Happy to have contributed to this new paper with a nice overview of the genes and pathways involved in fatty acid metabolism in Atlantic salmon. 

June 2022

• We have made some contributions to a new paper on characterization of 121 full length alleles of the enigmatic Vitellogenin protein in bees. Paper was led by Vilde Leipart and Gro Amdam.

• Final published verion of the first metbolic model of Atlantic salmon is out in PLOS Computational Biology. Great work by Jon Olav Vik and his team! 

• New preprint out led by Matilde M. Holen reveals interactions between chitin in the feed, microbial communities and endogenous chitin metabolism in Atlantic salmon. 

May 2022

• A new pre-print out on evolution of chitin metabolism associated genes in fish (mostly salmon). Great work by Matilde Mengkrog Holen!

April 2022

• Ohh...I got promotion to full professor :-)

• Great to finally have a in-person project meeting for the Improvafish team! Lots of interesting results about the feed-microbiome interaction in the salmon gut

March 2022

• Helle Tessland Baalsrud joined the lab as a postdoc on the EBP-Nor project. Welcome! 

January 2022

• We have started our efforts to help sequence all of Norways eukaryotic species together with all the partners in the EBP-Nor project

November 2021

• The former master student in our group Johanna Wagnerberger won the NMBU-award for the best master thesis 2020. Read the news story here, and if you  are interested in her research here is a link to her thesis. 

• Our paper on rediploidization following WGD across 100 million years is out in MBE. Study was led by Manu Gundappa and Dan Macqueen at Roslin Institute. Read the paper here.

August 2021

• Exciting to get this first paper on the curious genomes of sucker fish published. Much more to come on these duplicated genomes in the year(s) to come. Study led by Trevor Krabbenhoft group at University of Buffalo. Read the paper here.

• New preprint out on metabolic modelling of Atlantic salmon. Project is led by Jon Olav Vik at NMBU. Read the paper here.

June 2021

• Excited to be part of a huge 3M EUR grant funded by NRC to help sequence and assemble all eukaryote genomes (in the world!). Project is led by Kjetill Jakobsen at UiO. 

• Yeah! Our two fantastic master students Dom and Hanna defended their thesis projects with style. Congratulations to you both! 

• Happy to share our new pre-print about 100 million years of rediploidization dynamics following WGD in a salmonid ancestor. Study led by Manu Gundappa at the Roslin Institute. Read the paper here.

May 2021

• A new paper out in Frontiers in Immunology led by Alex West at the UiT ASTI centre. Single nuclei transcriptome view of the smoltifying gill in Atlantic salmon. Read the paper here.

April 2021

• Im proud of our new paper in Genome Biology. In collaboration with Rori Rholfs and Torgeir Hvidsten we use a comparative phylogenetic model to ask: how does selection shape genome regulatory evolution following whole genome duplication? Great computatinoal biology work by Gareth and Lars! Read the paper here.

March 2021

• Congratulations and thanks Yang Jin, for including me on this new paper using lipidomics to understand physiological remoddeling during life stage transition in Salmon. Read it here.

• Happy to see our new paper in G3 on 'print'. In this paper lead by Dave Hazlerigg at UiT we show how photoperiodic history affects how young salmon respond to changes in water salinity. Read it here.

• We wrote a pop-sci outreach piece on salmon and smoltification in Aftenposten Viten (in Norwegian). Read it here.

January 2021

• Our tallented PhD student Marius has gotten his first paper accepted (based on his master project). A very nice start on the new collaboration with Phil Pope and Torgeir Hvidsten on host-microbiome interactions. 

• What a great start to the new year! Johanna defended her master thesis on CRISPR based knock out characterization of abcg2 gene involved in salmon flesh coloration. Read her work here if you are interested.

December 2020

• Ragnhild Wilberg defended her master thesis today (10th December) ! She did a fantastic job. Congrats! If you are interested in transfection of primary liver cells in Atlantic salmon click here.

November 2020

• Finally out! An interesting collaboration between animal breeders, microbiologist and a genome guy (me). We found no/little/weak effects of salmon genetics on gut microbiota composition but we did find significant associations between salmon metabolism phenotypes and the gut microbiome. Now out in Microbiome!

• A fun collaboration between quantitative geneticists and omics people (i.e. us) reveal genetic architecture of salmon metabolism! Published in GSE.

October 2020

• Happy to have been part of this exciting new paper in PLOS Genetics, led by Shona Wood and Alex West at UiT. What happends to the circadian clock genes after a genome duplication?